Difference between revisions of "SLURM"
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| 32 | | 32 | ||
| Six-Core AMD Opteron(tm) Processor 2427 | | Six-Core AMD Opteron(tm) Processor 2427 | ||
| + | | | ||
|- | |- | ||
| − | | | + | | itp-big |
| 3 | | 3 | ||
| − | | | + | | 48 |
| − | | | + | | 144 |
| 128 | | 128 | ||
| AMD Opteron(tm) Processor 6172 | | AMD Opteron(tm) Processor 6172 | ||
| Line 75: | Line 76: | ||
| 256 | | 256 | ||
| Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz | | Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz | ||
| − | | | + | | Group Valenti |
|- | |- | ||
| fplo | | fplo | ||
| Line 83: | Line 84: | ||
| 256 | | 256 | ||
| Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | | Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | ||
| − | | | + | | Group Valenti |
|- | |- | ||
| dfg-xeon | | dfg-xeon | ||
| Line 91: | Line 92: | ||
| 128 | | 128 | ||
| Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | | Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | ||
| − | | | + | | Group Valenti |
| + | |- | ||
| + | | dfg-xeon | ||
| + | | 7 | ||
| + | | 20 | ||
| + | | 140 | ||
| + | | 128 | ||
| + | | Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz | ||
| + | | Group Valenti | ||
|- | |- | ||
| iboga | | iboga | ||
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|} | |} | ||
| − | Most nodes are for exclusive use by their corresponding owners. The itp and itp big nodes are for common usage. Except | + | Most nodes are for exclusive use by their corresponding owners. The itp and itp-big nodes are for common usage. Except for 'fplo' and 'dfg-big' nodes, all machines are connected with Infiniband for all traffic (IP and internode communitcation - MPI) |
== Submitting Jobs == | == Submitting Jobs == | ||
| − | In most | + | In most cases you want to submit a non interactive job to be executed in our cluster. |
This is very simple for serial (1 CPU) jobs: | This is very simple for serial (1 CPU) jobs: | ||
| Line 146: | Line 155: | ||
sbatch -p dfg -C infiniband -n X jobscript.sh | sbatch -p dfg -C infiniband -n X jobscript.sh | ||
| − | Note: Infiniband is | + | Note: Infiniband is not available for 'fplo' and 'dfg-big'. |
| − | Running '''SMP jobs''' (multiple threads, not necessary mpi). Running MPI jobs | + | Running '''SMP jobs''' (multiple threads, not necessary mpi). Running MPI jobs on a single node is recommended for the |
| − | dfg-big nodes. This are big host | + | dfg-big nodes. This are big host with up to 64 cpu's per node, but 'slow' gigabit network connection. Launch SMP jobs with |
sbatch -p PARTITION -N 1 -n X jobscript.sh | sbatch -p PARTITION -N 1 -n X jobscript.sh | ||
| Line 169: | Line 178: | ||
-t or --time=<time> | -t or --time=<time> | ||
| − | where time can | + | where time can be set in the format "days-hours". See man page for more formats. |
== Memory Management == | == Memory Management == | ||
| − | In Slurm you specify only one parameter, which is the limit for your real memory usage and drives the decision where your job is started. The virtual memory of your job maybe 2.5 times of your requested memory. You can exceed | + | In Slurm you specify only one parameter, which is the limit for your real memory usage and drives the decision where your job is started. The virtual memory of your job maybe 2.5 times of your requested memory. You can exceed your memory limit by 20%. But this will be swap space instead of real memory. This prevents crashing if you memory limit is a little to tight. |
== Inline Arguments == | == Inline Arguments == | ||
Latest revision as of 14:05, 15 November 2019
SLURM is the Simple Linux Utility for Resource Management and is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters.
Slurm is fully integrated in our system. You do not need set any environment variables.
Contents
Partitions
A partition is a subset of the cluster, a bundle of compute nodes with the same characteristics.
Based on access restrictions our cluster is divided in different partitions. 'sinfo' will only show partitions you are allowed to use. Using 'sinfo -a' shows all partitons.
A partition is selected by '-p PARTITIONNAME'.
| Partition | No. Nodes | Cores/M | Tot. Cores | RAM/GB | CPU | Remark/Restriction |
|---|---|---|---|---|---|---|
| itp | 10 | 12 | 120 | 32 | Six-Core AMD Opteron(tm) Processor 2427 | |
| itp-big | 3 | 48 | 144 | 128 | AMD Opteron(tm) Processor 6172 | |
| dfg-big | 3 | 32 | 96 | 128 | 8-Core AMD Opteron(tm) Processor 6128 | Group Valenti |
| dfg-big | 3 | 48 | 144 | 128/256 | 12-Core AMD Opteron(tm) Processor 6168 | Group Valenti |
| dfg-big | 4 | 64 | 256 | 128/256 | 16-Core AMD Opteron(tm) Processor 6272 | Group Valenti |
| dfg-big | 4 | 48 | 192 | 128/256 | 12-Core AMD Opteron(tm) Processor 6344 | Group Valenti |
| fplo | 2 | 12 | 24 | 256 | Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz | Group Valenti |
| fplo | 4 | 16 | 32 | 256 | Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | Group Valenti |
| dfg-xeon | 5 | 16 | 32 | 128 | Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz | Group Valenti |
| dfg-xeon | 7 | 20 | 140 | 128 | Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz | Group Valenti |
| iboga | 44 | 20 | 880 | 64 | Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz | Group Rezzolla |
| dreama | 1 | 40 | 40 | 1024 | Intel(R) Xeon(R) CPU E7-4820 v3 @ 1.90GHz | Group Rezzolla |
| barcelona | 8 | 40 | 320 | 192 | Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz | Group Valenti |
Most nodes are for exclusive use by their corresponding owners. The itp and itp-big nodes are for common usage. Except for 'fplo' and 'dfg-big' nodes, all machines are connected with Infiniband for all traffic (IP and internode communitcation - MPI)
Submitting Jobs
In most cases you want to submit a non interactive job to be executed in our cluster.
This is very simple for serial (1 CPU) jobs:
sbatch -p PARTITION jobscript.sh
where jobscript.sh is a shell script with your job commands.
Running openMPI jobs is not much more complictated:
sbatch -p PARTITION -n X jobscript.sh
where X is the number of desired MPI processes. Launch the job in the jobscript with:
mpirun YOUREXECUTABLE
You don't have to worry about the number of processes or specific nodes. Both slurm and openmpi know about each other.
If you want infiniband for your MPI job (which is usually a good idea, if not running on the same node), you have to request the feature infiniband:
sbatch -p dfg -C infiniband -n X jobscript.sh
Note: Infiniband is not available for 'fplo' and 'dfg-big'.
Running SMP jobs (multiple threads, not necessary mpi). Running MPI jobs on a single node is recommended for the dfg-big nodes. This are big host with up to 64 cpu's per node, but 'slow' gigabit network connection. Launch SMP jobs with
sbatch -p PARTITION -N 1 -n X jobscript.sh
Differences in network the network connection
The new v3 dfg-xeon nodes are equipped with 10 GB network. This is faster (trough put) and has lower latency then gigabit ethernet, but is not is not as fast as the DDR infinband network. The 10 GB network is used for MPI and I/O. Infiniband is only use for MPI.
Defining Resource limits
By default each job allocates 2 GB memory and a run time of 3 days. More resources can be requested by
--mem-per-cpu=<MB>
where <MB> is the memory in megabytes. The virtual memory limit is 2.5 times of the requested real memory limit.
The memory limit is not a hard limit. When exceeding the limit, your memory will be swapped out. Only when using more the 150% of the limit your job will be killed. So be conservative, to keep enough room for other jobs. Requested memory is blocked from the use by other jobs.
-t or --time=
where time can be set in the format "days-hours". See man page for more formats.
Memory Management
In Slurm you specify only one parameter, which is the limit for your real memory usage and drives the decision where your job is started. The virtual memory of your job maybe 2.5 times of your requested memory. You can exceed your memory limit by 20%. But this will be swap space instead of real memory. This prevents crashing if you memory limit is a little to tight.
Inline Arguments
sbatch arguments can be written in the jobfile:
#! /bin/bash # # Choosing a partition: #SBATCH -p housewives YOUR JOB COMMANDS....
Links
- SLURM-Homepage [1]
